With the acceleration of urbanization, passenger traffic on urban rail transit has proliferated rapidly, emerging as a significant source of urban energy consumption and impacting the efficient operation and sustainable development of urban rail transit systems. In the field of multi-train cooperative energy-saving operation for urban rail transit, previous research has faced two main challenges: First, studies often indirectly represent regenerative braking energy recovery rate through the overlap time of “traction-braking” phases, neglecting to account for intuitively demonstrating energy-saving effects. Second, research has predominantly centered on mathematical formulation and algorithmic development, neglecting practical engineering constraints and failing to adequately assess the viability of implementing operational plans in real-world scenarios. To bridge these identified gaps, this study fully integrates the characteristics of power supply sections with the spatiotemporal coupling of train operations. It analyzes the interaction scenarios of regenerative braking energy among all up- and down-bound trains within the same power supply zone that influence each other. Employing the spatiotemporal network modeling method, a three-dimensional space-time-speed grid network framework is constructed. The global train operation time and state are discretized, and the objective function is formulated to minimize the net energy consumption of train operations. A mixed-integer programming (MIP) model is developed subject to various constraints such as departure intervals, stop durations, safety tracking, and additional operational constraints. The resulting solution is an energy-optimized urban rail train timetable and operational diagram. Numerical experiments are conducted in engineering scenarios to verify the efficacy of this approach, thereby establishing a generalized framework for energy-saving optimization in actual urban rail transit lines. Two solution methods based on the constructed model are proposed for different engineering applications, ensuring safety, operational efficiency, and energy sustainability of urban rail transit operations.